Research workbench
The crystal structure of dps, a ferritin homolog that binds and protects DNA
Analyse The crystal structure of dps, a ferritin homolog that binds and protects DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DPS
- Type
- protein
- Length
- 1,855 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps
- UniProt
- P0ABT2
- Ligands
- NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dps | protein | 159 | 71% helix, 1% strand | P0ABT2 |
| B, C, E, F, G, H, I, J, K, L | Dps | protein | 154 | 74% helix, 1% strand | P0ABT2 |
| D | Dps | protein | 156 | 72% helix, 1% strand | P0ABT2 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.76 | 0.98 | 20 | empty |
| 2 | 85 | 0.76 | 0.97 | 21 | empty |
| 3 | 73 | 0.75 | 0.98 | 21 | empty |
| 4 | 82 | 0.75 | 0.97 | 20 | empty |
| 5 | 71 | 0.75 | 0.98 | 21 | empty |
Interfaces
30 interfaces between chains.
- E–G · 1611 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1609 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1608 Ų buried · 18 hydrogen bonds · protein-protein
- I–K · 1606 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1606 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1DPS · The crystal structure of dps, a ferritin homolog that binds and protects DNA · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0ABT2
- Elsewhere: RCSB PDB 1DPS · PDBe 1DPS · UniProt P0ABT2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.